This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Mass spectrometry is a method of choice for quantifying low abundance proteins and peptides and it has been applied to many areas of biology. We are developing a range of computational methods for protein and peptide quantification, including methods for finding and integrating peaks of interest, and detecting interference to obtain a robust measure of the amount of material present in the samples. G. Zhang, B.M. Ueberheide, S. Waldemarson, S. Myung, K. Molloy, J. Eriksson, B.T. Chait, T.A. Neubert, and D. Feny[unreadable], "Protein Quantitation Using Mass Spectrometry", Methods in Molecular Biology, Computational Biology, Ed. D. Feny[unreadable], Humana Press, Totowa, NJ, in press 2010.